In a statement on Monday night, the military said the two planes were from the USS Carl Vinson. The status of the crew is unknown and a search effort is under way.
"Contact was lost with two US Marine F/A-18 Hornet jets flying over Iraq," said Nick Minecci, a staff sergeant at the US military's press centre in Baghdad.
Contact was lost at 10.10pm (1810 GMT) on Monday, the statement confirmed.
There was "no initial indication of hostile fire" involved in the incident, he said.
There were unconfirmed reports that the two fighter jets might have collided.
The military could not immediately say whether the planes were single or two-seaters.
The US military said it had no further information to release.